Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   101786
Name   oriT_pXFAS01.CFBP8430 in_silico
Organism   Xylella fastidiosa subsp. multiplex strain CFBP8430
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_JAJKGO010000004 (4894..4999 [-], 106 nt)
oriT length   106 nt
IRs (inverted repeats)      68..74, 77..83  (CACCGGA..TCCGGTG)
Location of nic site      _
Conserved sequence flanking the
  nic site    		  _
Note   Predicted by oriTfinder 2.0

  oriT sequence  


Download         Length: 106 nt

>oriT_pXFAS01.CFBP8430
GCTAGCCTCGCAGAGCAGGATTCCCGTTGAGTACCGAAGGTGCGAATAAGGGAAAGTGAAGAAGGAACACCGGATTTCCGGTGGGCCTACTTCACATATCCTGCCC

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   1499 GenBank   WP_004086668
Name   Relaxase_LOK80_RS13085_pXFAS01.CFBP8430 insolico UniProt ID   B2IAU3
Length   830 a.a. PDB ID   
Note   Predicted by oriTfinder 2.0

  Relaxase protein sequence


Download         Length: 830 a.a.        Molecular weight: 92664.59 Da        Isoelectric Point: 10.5711

>WP_004086668.1 TraI/MobA(P) family conjugative relaxase [Xylella fastidiosa]
MIAKHVPMRVVKKSDFRELVKYLSNQQGKQERVGCVTVTNCFQNNVLDAALEVQATQALNTRSEADKTYH
LLISFREGENPAPEILEVIESRVCAALGYADYQRVSVVHHDTDNLHIHVAINKIHPKSYTIHTPYNDYKT
LGEICKKLEREYGLEADNHTVRKTVGENRADDMERNAGVESLLGWIKRECTDQIKQVQSWSELHAVMQRN
GLEIRERGNGLVITNGVGRSVKASSVARDFSKAKLEARFGAFESFVKQAPSVSSVHARRIQAPLVEKVGR
RPPPRSKGRTPSLSSVGVLHVNSGIRYEQRPIYVKQASTAELYAMYKLEQQDLGAVRNVAIARARTKRDR
KIEATKRLGRIKRAAIKLMRGPGVNKKLLYALARKSLKEGVEKANTDYLKARDAAYATYHRRVWADWLQV
QATQGNAEALAALRAREMRQWWSCNIFGGLQARRTGPVPGLKPDNITKAGTIIYRVGSTAIRDDGDLLNV
SHGAGDYGVEAALRMAMYRYGERITVKGSDEFKKRVVQIAAAARLNISFDDEVLDKRRKQLVSDAAVIVK
LTDAMLSDKTAQFTQAQASRVGAFQEDALSEYDAAISRSINLANQEQINEQQRTRAKHYFVQRWSDRGGP
NSRRDGHATRIRSGGGGSGKHGASGATVISSAGGFNKPNVGGIGAKPPPASTHRLRNLHQLGVVQFSRGS
EVLLPRHVSDCVGEQQTERNHRVRRDVHTAGITSSELMAVDKYIAERELKRVREFDIMKNRRYNEDDAGM
VKFAGLRQVDGKSLVLLKRNDEVIVLAIDVATARRMKRFSLGDEVLLTKKGTLKTKGRNR

  Protein domains


Predicted by InterproScan.

Relaxase/Mobilisation nuclease domain (Relaxase)

(12-250)

Large polyvalent protein-associated domain 7 (LPD7)

(463-550)


  Protein structure


Source ID Structure
AlphaFold DB B2IAU3


T4CP

ID   1176 GenBank   WP_004086666
Name   t4cp2_LOK80_RS13090_pXFAS01.CFBP8430 insolico UniProt ID   _
Length   644 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 644 a.a.        Molecular weight: 72064.60 Da        Isoelectric Point: 8.5739

>WP_004086666.1 type IV secretory system conjugative DNA transfer family protein [Xylella fastidiosa]
MRKPNNAVGPQVRGGQRKKNKLVPALALTSMATGLQVATQYFAHTFNYQSTLGGNYNHIYAPWSILSWYA
KWGDQFHNYFFAAGNIGMMVTAGGLIGTALIKTFEINSVKANEYLHGSACWASKKDIEQSGLLGNDEGVY
VGAWEDKDGRLHYLRHNGPEHVLTYAPTRSGKGVGLVVPTLLSWPHSVVVTDLKGELWAMTAGWRQKHAK
NKVIRFEPATLNGSVCWNPLDEIRIGTEYEVGDVQNLATLIVDPNGKGLESHWQKTSQALLVGVILHVLY
KRKNEGFPATLSYVDHIMSDPNRNVAELWMEMTQYGHINGENHPAVGSAGRDMMDRPEEEAGSVLSTAKS
YIALYRDPVVARNVSKSDFCIKDLMNHDDPVSLYIVTQPNDKGRLRPLVRVMLNMIVRLLADKMKFERVP
TELSWWRQILTKLGFNQVADFHVRSKKSYKHRLLGMIDEFPSLGKLEIMQESLAFVAGYGIKFYLICQDL
NQLKSRETGYGPDETITSNCHVQNAYPPNRVETAEHLSKLTGQTTVLKEQITTSGKRATPILGQLSRTIQ
EVQRPLLTVDECLRMPGPKKDAEGQITEAGDMVVYVAGYPAIYGKQPLYFQDPIFIARAAVPEPKTSDTL
RLVHEPTLLDEIKI

  Protein domains


Predicted by InterproScan.

Type IV secretory system Conjugative DNA transfer (T4SS-DNA_transf)

(429-627)

Type IV secretory system Conjugative DNA transfer (T4SS-DNA_transf)

(119-417)

  Protein structure



No available structure.



ID   1177 GenBank   WP_004086690
Name   t4cp2_LOK80_RS13190_pXFAS01.CFBP8430 insolico UniProt ID   _
Length   854 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 854 a.a.        Molecular weight: 95956.03 Da        Isoelectric Point: 6.3394

>WP_004086690.1 conjugal transfer protein TrbE [Xylella fastidiosa]
MFQIITIAIALLGTVLLIWLFLLVQRANADLRLKNHRSKDAGLADLLNYAAVVDDGVIVGKNGSFMASWL
YRGADNASATEAERELISFRINQALASFDNAWMVHVDAVRRPAPSYSDPSLSHFPDAVSAAVDEERRRLF
ESIDTLYEGFFVVTVTWFPPVLAERRFVELMFHDDAEKPNDKTRTAHLIDHFKREVINLENRLSLAVELE
RLRGVKITKEDGSTVTHDQQLQWLHFCVTGLNHPIQLPSNPMYIDSLIGGQELYPGVVPKIGRNFIQVVA
IEGFPLESYPGILSVLAELPIEYRWSSRFIFLDHHEAVSHLEKFRKKWKQKMRGFFDQVFNTNTSHVDED
AVSMVADASSAIAETNSGLVSQGYYTSVVVLMNESREQVEQSARRLEKAINALAFTARVETINTMDAYLG
SLPGHGVENVRRPLLNTMNFADLLPTSTIWTGENRAPSPLFPPNAPPLLHGVTSGNSPMRINLHVRDLGH
CIIFGPTRTGKSTKLALVAFQWRRYLGARIYAFDKGLSMYPTCKAMHGHHFSIASNTDKLAFAPLSRLDT
RTRRAWAMEWIDTILALNGVITSPAQRNAIAEAILSMSKSKASTLSEFIVTVQDEVIREALKPYTVDGNM
GYLLDAVEDGLELADFMTFEIEQLMGLGEKFALPVLLYLFMRIEESLSEEDARPTLLILDEAWLMLSHTT
FRDKIEEWLRSMAKKNCSVLMATQSISEAAKSGILDIITESTACRIFLANPNAREEKTAEIYGRLGLNNR
QIEIIASAVPKRDYYYVSEKGRRLYQLALGPLALAFVGSTDKESIAMIRKLEALHGDAWVHEWLRLKGLR
LDEYVSPNDYGVAA

  Protein domains


Predicted by InterproScan.

TraG P-loop domain (P-loop_TraG)

(619-778)

CagE, TrbE, VirB family, component of type IV transporter system (CagE_TrbE_VirB)

(220-431)

  Protein structure



No available structure.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 23481..33662

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
LOK80_RS13125 (LOK80_13070) 18780..19094 - 315 WP_012382835 TrfB-related DNA-binding protein -
LOK80_RS13130 (LOK80_13075) 19162..19629 - 468 WP_272695929 hypothetical protein -
LOK80_RS13135 (LOK80_13080) 20565..21128 - 564 WP_004086710 recombinase family protein -
LOK80_RS13140 (LOK80_13085) 21671..22039 + 369 WP_004086708 hypothetical protein -
LOK80_RS13145 (LOK80_13090) 22036..22263 + 228 WP_004086706 hypothetical protein -
LOK80_RS13150 (LOK80_13095) 22876..23475 - 600 WP_004086719 conjugal transfer protein TrbN -
LOK80_RS13155 (LOK80_13100) 23481..24851 - 1371 WP_004086703 P-type conjugative transfer protein TrbL virB6
LOK80_RS13160 (LOK80_13105) 24873..25109 - 237 WP_012382834 EexN family lipoprotein -
LOK80_RS13165 (LOK80_13110) 25126..25899 - 774 WP_004086702 P-type conjugative transfer protein TrbJ virB5
LOK80_RS13170 (LOK80_13115) 25918..27318 - 1401 WP_012382833 TrbI/VirB10 family protein virB10
LOK80_RS13175 (LOK80_13120) 27324..27800 - 477 WP_004086697 conjugal transfer protein TrbH -
LOK80_RS13180 (LOK80_13125) 27803..28693 - 891 WP_004086695 P-type conjugative transfer protein TrbG virB9
LOK80_RS13185 (LOK80_13130) 28710..29426 - 717 WP_004086692 conjugal transfer protein TrbF virB8
LOK80_RS13190 (LOK80_13135) 29423..31987 - 2565 WP_004086690 conjugal transfer protein TrbE virb4
LOK80_RS13195 (LOK80_13140) 31975..32295 - 321 WP_004086725 conjugal transfer protein TrbD virB3
LOK80_RS13200 (LOK80_13145) 32298..32690 - 393 WP_004086717 TrbC/VirB2 family protein virB2
LOK80_RS13205 (LOK80_13150) 32703..33662 - 960 WP_038231439 P-type conjugative transfer ATPase TrbB virB11
LOK80_RS13210 (LOK80_13155) 33869..34225 - 357 WP_012382841 transcriptional regulator -
LOK80_RS13215 (LOK80_13160) 34343..34702 + 360 WP_012382840 single-stranded DNA-binding protein -
LOK80_RS13220 (LOK80_13165) 34746..35102 + 357 WP_004086687 hypothetical protein -
LOK80_RS13225 (LOK80_13170) 35124..36035 + 912 WP_004086685 replication protein RepA -
LOK80_RS13230 (LOK80_13175) 36756..37076 + 321 WP_012382839 KleE stable inheritance protein -
LOK80_RS13235 (LOK80_13180) 37117..38313 - 1197 WP_004086683 RNA-guided endonuclease TnpB family protein -
LOK80_RS13240 (LOK80_13185) 38307..38561 - 255 Protein_40 recombinase family protein -

Host bacterium

ID   2230 GenBank   NZ_JAJKGO010000004
Plasmid name   pXFAS01.CFBP8430 Incompatibility group   -
Plasmid size   38772 bp Coordinate of oriT [Strand]   4894..4999 [-]
Host baterium   Xylella fastidiosa subsp. multiplex strain CFBP8430

Cargo genes

Drug resistance gene   -
Virulence gene   -
Metal resistance gene   -
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -